BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 30053

Title: Solution NMR structure of PT-free dsDNA from Streptomyces lividans   PubMed: 27169778

Authors: Lan, Wenxian; Cao, Chunyang

Citation: Lan, Wenxian; Hu, Zhongpei; Cao, Chunyang. "Structural investigation into physiological DNA phosphorothioate modification"  Sci. Rep. 6, 25737-25737 (2016).

Assembly members:
DNA (5'-D(*CP*GP*GP*CP*CP*GP*CP*CP*GP*A)-3'), polymer, 10 residues, 3030.981 Da.
DNA (5'-D(*TP*CP*GP*GP*CP*GP*GP*CP*CP*G)-3'), polymer, 10 residues, 3061.992 Da.

Natural source:   Common Name: high GC Gram+   Taxonomy ID: 1916   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Streptomyces lividans

Experimental source:   Production method: recombinant technology   Host organism: Streptomyces lividans

Entity Sequences (FASTA):
DNA (5'-D(*CP*GP*GP*CP*CP*GP*CP*CP*GP*A)-3'): CGGCCGCCGA
DNA (5'-D(*TP*CP*GP*GP*CP*GP*GP*CP*CP*G)-3'): TCGGCGGCCG

Data sets:
Data typeCount
1H chemical shifts156
31P chemical shifts16

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 10 residues - 3030.981 Da.

1   DCDGDGDCDCDGDCDCDGDA

Entity 2, entity_2 10 residues - 3061.992 Da.

1   DTDCDGDGDCDGDGDCDCDG

Samples:

sample_1: NaCl 100 mM; NaPO4 40 mM; PT-free dsDNA, none, 1.0 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 360 mM; pH: 7.0; pressure: 1.0 atm; temperature: 298 K

sample_conditions_2: ionic strength: 360 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1anisotropicsample_conditions_1
2D 1H-1H TOCSYsample_1anisotropicsample_conditions_2
2D DQF-COSYsample_1anisotropicsample_conditions_2
2D NOESYsample_1anisotropicsample_conditions_2
2D 1H-31P hetcorsample_1anisotropicsample_conditions_2

Software:

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

  • Agilent DD2 600 MHz
  • Agilent DD2 500 MHz

Related Database Links: